opencb · juanfeSanahuja · Feb 5, 2024 · Feb 2, 2024
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2024-01-30 OpenCB
+* Copyright 2015-2024-02-02 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2024-01-30 OpenCB
+* Copyright 2015-2024-02-02 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java
@@ -106,7 +106,11 @@ private RestResponse<String> model() throws Exception {
         logger.debug("Executing model in Meta command line");
 
         MetaCommandOptions.ModelCommandOptions commandOptions = metaCommandOptions.modelCommandOptions;
-        return openCGAClient.getMetaClient().model();
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("model", commandOptions.model);
+
+        return openCGAClient.getMetaClient().model(queryParams);
     }
 
     private RestResponse<String> ping() throws Exception {

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/MetaCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/MetaCommandOptions.java
@@ -87,6 +87,9 @@ public class ModelCommandOptions {
         @ParametersDelegate
         public CommonCommandOptions commonOptions = commonCommandOptions;
 
+        @Parameter(names = {"--model"}, description = "Model description", required = false, arity = 1)
+        public String model; 
+
     }
 
     @Parameters(commandNames = {"ping"}, commandDescription ="Ping Opencga webservices.")

diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R
@@ -5,17 +5,17 @@ setGeneric("userClient", function(OpencgaR, user, users, filterId, endpointName,
 
 # ##############################################################################
 ## ProjectClient
-setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...)
+setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...)
     standardGeneric("projectClient"))
 
 # ##############################################################################
 ## StudyClient
-setGeneric("studyClient", function(OpencgaR, studies, members, templateId, study, variableSet, group, endpointName, params=NULL, ...)
+setGeneric("studyClient", function(OpencgaR, members, study, group, variableSet, templateId, studies, endpointName, params=NULL, ...)
     standardGeneric("studyClient"))
 
 # ##############################################################################
 ## FileClient
-setGeneric("fileClient", function(OpencgaR, members, folder, file, files, annotationSet, endpointName, params=NULL, ...)
+setGeneric("fileClient", function(OpencgaR, members, folder, file, annotationSet, files, endpointName, params=NULL, ...)
     standardGeneric("fileClient"))
 
 # ##############################################################################
@@ -30,17 +30,17 @@ setGeneric("sampleClient", function(OpencgaR, annotationSet, members, sample, sa
 
 # ##############################################################################
 ## IndividualClient
-setGeneric("individualClient", function(OpencgaR, members, annotationSet, individuals, individual, endpointName, params=NULL, ...)
+setGeneric("individualClient", function(OpencgaR, individual, annotationSet, members, individuals, endpointName, params=NULL, ...)
     standardGeneric("individualClient"))
 
 # ##############################################################################
 ## FamilyClient
-setGeneric("familyClient", function(OpencgaR, members, annotationSet, families, family, endpointName, params=NULL, ...)
+setGeneric("familyClient", function(OpencgaR, families, annotationSet, members, family, endpointName, params=NULL, ...)
     standardGeneric("familyClient"))
 
 # ##############################################################################
 ## CohortClient
-setGeneric("cohortClient", function(OpencgaR, cohort, annotationSet, members, cohorts, endpointName, params=NULL, ...)
+setGeneric("cohortClient", function(OpencgaR, annotationSet, members, cohort, cohorts, endpointName, params=NULL, ...)
     standardGeneric("cohortClient"))
 
 # ##############################################################################
@@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## ClinicalClient
-setGeneric("clinicalClient", function(OpencgaR, members, interpretations, clinicalAnalysis, interpretation, annotationSet, clinicalAnalyses, endpointName, params=NULL, ...)
+setGeneric("clinicalClient", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, annotationSet, clinicalAnalyses, endpointName, params=NULL, ...)
     standardGeneric("clinicalClient"))
 
 # ##############################################################################

diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -61,7 +61,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("clinicalClient", "OpencgaR", function(OpencgaR, members, interpretations, clinicalAnalysis, interpretation, annotationSet, clinicalAnalyses, endpointName, params=NULL, ...) {
+setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, annotationSet, clinicalAnalyses, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update:

diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohort, annotationSet, members, cohorts, endpointName, params=NULL, ...) {
+setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, members, cohort, cohorts, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update:

diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -38,7 +38,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("familyClient", "OpencgaR", function(OpencgaR, members, annotationSet, families, family, endpointName, params=NULL, ...) {
+setMethod("familyClient", "OpencgaR", function(OpencgaR, families, annotationSet, members, family, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/families/acl/{members}/update:

diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -54,7 +54,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("fileClient", "OpencgaR", function(OpencgaR, members, folder, file, files, annotationSet, endpointName, params=NULL, ...) {
+setMethod("fileClient", "OpencgaR", function(OpencgaR, members, folder, file, annotationSet, files, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/files/acl/{members}/update:

diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("individualClient", "OpencgaR", function(OpencgaR, members, annotationSet, individuals, individual, endpointName, params=NULL, ...) {
+setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, annotationSet, members, individuals, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update:

diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -23,7 +23,7 @@
 #' | about | /{apiVersion}/meta/about |  |
 #' | api | /{apiVersion}/meta/api | category |
 #' | fail | /{apiVersion}/meta/fail |  |
-#' | model | /{apiVersion}/meta/model |  |
+#' | model | /{apiVersion}/meta/model | model |
 #' | ping | /{apiVersion}/meta/ping |  |
 #' | status | /{apiVersion}/meta/status |  |
 #'
@@ -56,7 +56,7 @@ setMethod("metaClient", "OpencgaR", function(OpencgaR, endpointName, params=NULL
 
         #' @section Endpoint /{apiVersion}/meta/model:
         #' Opencga model webservices.
-
+        #' @param model Model description.
         model=fetchOpenCGA(object=OpencgaR, category="meta", categoryId=NULL, subcategory=NULL, subcategoryId=NULL,
                 action="model", params=params, httpMethod="GET", as.queryParam=NULL, ...),
 

diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -34,7 +34,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("projectClient", "OpencgaR", function(OpencgaR, project, projects, endpointName, params=NULL, ...) {
+setMethod("projectClient", "OpencgaR", function(OpencgaR, projects, project, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/projects/create:

diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -46,7 +46,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("studyClient", "OpencgaR", function(OpencgaR, studies, members, templateId, study, variableSet, group, endpointName, params=NULL, ...) {
+setMethod("studyClient", "OpencgaR", function(OpencgaR, members, study, group, variableSet, templateId, studies, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/studies/acl/{members}/update:

diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-01-30
+#    Autogenerated on: 2024-02-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java
@@ -36,7 +36,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2024-01-30
+* Autogenerated on: 2024-02-02
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java
@@ -40,7 +40,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2024-01-30
+* Autogenerated on: 2024-02-02
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/...a-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/...a-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java
@@ -54,7 +54,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2024-01-30
+* Autogenerated on: 2024-02-02
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java
@@ -37,7 +37,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2024-01-30
+* Autogenerated on: 2024-02-02
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java
@@ -35,7 +35,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2024-01-30
+* Autogenerated on: 2024-02-02
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java
@@ -36,7 +36,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2024-01-30
+* Autogenerated on: 2024-02-02
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java
@@ -43,7 +43,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2024-01-30
+* Autogenerated on: 2024-02-02
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.

diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java
@@ -27,7 +27,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2024-01-30
+* Autogenerated on: 2024-02-02
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.